Population analysis of the Shih Tzu breed Genetic analysis of the Kennel Club pedigree records of the UK Shih Tzu population has been carried out with the aim of estimating the rate of loss of genetic diversity within the breed and providing information to guide a future sustainable breeding strategy. The population statistics summarised provide a picture of trends in census size, the number of animals used for breeding, the rate of inbreeding and the estimated effective population size. The rate of inbreeding and estimated effective population size indicate the rate at which genetic diversity is being lost within the breed. The analysis also calculates the average relationship (kinship) among all individuals of the breed born per year and is used to determine the level of inbreeding that might be expected if matings were made among randomly selected dogs from the population (the expected rate of inbreeding). Summary of results The analysis utilises the complete computerised pedigree records for the current UK Kennel Club registered Shih Tzu population, and statistics were calculated for the period 1980-2014. 1
Figure 1: a plot of number of registrations by year of birth, indicative of any changing trend in popularity of the breed, followed by the yearly trend in number of animals registered (and 95% confidence interval). Breed: Shih Tzu Figure 1: Number of registrations by year of birth Trend of registrations over year of birth (1980-2014) = 101.58 per year (with a 95% confidence interval of 70.55 to 132.61). 2
Table 1: census statistics by year, including sire use statistics. Table 1: by year (1980-2014), the number of registered puppies born, by the number of unique dams and sires; maximum, median, mode, mean and standard deviation of number of puppies per sire; and the percentage of all puppies born to the most prolific 50%, 25%, 10% and 5% of sires. year #born #dams #sires puppies per sire %puppies sired by most prolific sires max median mode mean sd 50% sires 25% sires 10% sires 5% sires 1980 414 300 206 12 1 1 2.01 1.69 75.12 51.93 31.16 18.84 1981 1085 515 308 24 2 1 3.52 3.69 82.4 59.54 35.94 22.3 1982 1404 570 329 28 3 1 4.27 4.53 82.48 59.97 35.68 22.29 1983 1471 581 317 36 3 2 4.64 4.55 79.95 56.83 33.45 21.07 1984 1554 640 323 29 3 1 4.81 4.81 82.05 59.46 33.4 20.33 1985 1641 654 333 39 3 1 4.93 5.17 81.72 59.35 35.47 22.55 1986 1618 679 326 39 3 1 4.96 5.39 82.57 59.83 35.54 22.56 1987 1806 739 332 58 4 1 5.44 6.09 82.06 59.91 35.88 23.75 1988 2059 778 362 30 4 2 5.69 5.3 81.64 58.47 31.37 18.65 1989 3963 994 383 121 6 2 10.35 14.3 84.71 64.62 41.21 28.51 1990 4525 1077 448 140 5 5 10.1 14.11 83.98 65.1 41.68 27.58 1991 4183 984 443 102 6 4 9.44 11.97 83.39 63.38 39.59 26.8 1992 4268 1032 455 104 5 4 9.38 12.3 83.29 64.13 41.19 28.19 1993 4055 978 466 131 5 4 8.7 10.91 82.17 61.13 37.71 24.93 1994 4631 1112 508 97 6 4 9.12 10.78 83.26 61.87 37.66 24.53 1995 4486 1115 536 79 5 4 8.37 10.27 82.37 61.44 39.1 26.53 1996 4753 1139 572 74 5 5 8.31 9.37 80.81 59.69 36.69 24.78 1997 4155 1001 496 68 5 4 8.38 9.03 81.68 59.98 35.43 22.89 1998 4228 1011 520 96 5.5 4 8.13 8.32 81.05 57.12 32.47 20.96 1999 3769 920 503 86 5 4 7.49 7.5 79.28 56.86 32.13 20.83 2000 3420 838 442 101 5 5 7.74 8.62 78.77 56.67 33.54 22.63 2001 3208 808 436 71 5 2 7.36 7.07 79.89 56.27 31.86 19.86 2002 3258 806 444 57 5 4 7.34 6.85 78.33 56.08 32.01 19.74 2003 3297 830 463 57 5 4 7.12 7.01 79.44 56.87 33.06 20.96 2004 3313 808 440 39 5 5 7.53 6.67 79.54 56.66 31.09 18.38 2005 3942 945 482 64 6 4 8.18 8.17 80.34 57.99 33.84 21.06 2006 4437 993 501 82 6 5 8.86 8.83 80.39 57.94 33.49 20.76 2007 5247 1135 564 121 6 4 9.3 10.95 80.98 59.48 36.52 24.41 2008 5351 1201 618 84 6 4 8.66 8.15 79.24 55.82 31.66 20.09 2009 5189 1157 631 65 6 4 8.22 7.62 78.17 55.64 31.7 20.02 2010 5129 1130 642 58 6 5 7.99 7.23 77.85 54.94 31.57 19.54 2011 4965 1124 626 63 6 5 7.93 7.13 78.99 55.71 30.88 18.83 2012 4567 1025 575 55 5 4 7.94 7.94 79.88 58.4 34.99 21.94 2013 4200 960 550 77 5 5 7.64 7.6 79.26 56.52 32.43 20.9 2014 3855 854 474 50 6 5 8.13 7.43 76.89 55.15 32.01 20.75 3
Generation interval: the mean average age (in years) of parents at the birth of offspring which themselves go on to reproduce. Mean generation interval (years) = 3.63 Figure 2: a plot of the annual mean observed inbreeding coefficient (showing loss of genetic diversity), and mean expected inbreeding coefficient (from random mating ) over the period 1980-2014. Expected inbreeding is staggered by the generation interval and, where >2000 animals are born in a single year, the 95% confidence interval is indicated. Figure 2: Annual mean observed and expected inbreeding coefficients 4
Estimated effective population size: the rate of inbreeding (slope or steepness of the observed inbreeding in Figure 2) is used to estimate the effective population size of the breed. The effective population size is the number of breeding animals in an idealised, hypothetical population that would be expected to show the same rate of loss of genetic diversity (rate of inbreeding) as the breed in question. It may be thought of as the size of the gene pool of the breed. Below an effective population size of 100 (inbreeding rate of 0.50% per generation) the rate of loss of genetic diversity in a breed/population increases dramatically (Food & Agriculture Organisation of the United Nations, Monitoring animal genetic resources and criteria for prioritization of breeds, 1992). An effective population size of below 50 (inbreeding rate of 1.0% per generation) indicates the future of the breed many be considered to be at risk (Food & Agriculture Organisation of the United Nations, Breeding strategies for sustainable management of animal genetic resources, 2010). Where the rate of inbreeding is negative (implying increasing genetic diversity in the breed), effective population size is denoted n/a. Estimated effective population size = 170.1 NB - this estimate is made using the rate of inbreeding over the whole period 1980-2014 5
Table 2: a breakdown of census statistics, sire and dam usage and indicators of the rate of loss of genetic diversity over 5 year periods (1980-4, 1985-9, 1990-4, 1995-9, 2000-4, 2005-9, 2010-14). Rate of inbreeding and estimated effective population size for each 5-year block can be compared with the trend in observed inbreeding in Figure 2. Table 2: by 5-year blocks, the mean number of registrations; for sires the total number used, maximum, mean, median, mode, standard deviation and skewness (indicative of the size of the tail on the distribution) of number of progeny per sire; for dams the total number used, maximum, mean, median, mode, standard deviation and skewness of number of progeny per dam; rate of inbreeding per generation (as a decimal, multiply by 100 to obtain as a percentage); mean generation interval; and estimated effective population size. years 1980-1984 1985-1989 1990-1994 1995-1999 2000-2004 2005-2009 2010-2014 mean #registrations 1185.6 2217.4 4332.4 4278.2 3299.2 4833.2 4543.2 Total #sires 804 906 1213 1419 1207 1517 1612 Max #progeny 102 151 425 355 172 261 198 Mean #progeny 7.3682 12.236 17.855 15.07 13.664 15.929 14.091 Median #progeny 4 6 7 6 7 8 7 Mode #progeny 1 1 4 4 5 5 5 SD #progeny 10.622 18.518 33.5 25 18.092 22.799 18.675 Skew #progeny 3.4178 3.6179 5.7677 5.3463 3.2893 4.3619 3.6323 Total #dams 1733 2444 3204 3319 2746 3482 3496 Max #progeny 19 24 34 38 33 33 31 Mean #progeny 3.4183 4.536 6.7597 6.4429 6.0069 6.94 6.4971 Median #progeny 3 4 5 5 5 5 5 Mode #progeny 1 1 4 4 4 5 5 SD #progeny 2.6795 3.3256 5.1166 4.838 4.2898 5.0084 4.3654 Skew #progeny 1.6967 1.4196 1.6133 1.6735 1.4532 1.4185 1.3755 Rate of inbreeding 0.025155 0.000436 0.004731 0.009354-0.00988-0.00644-0.01171 Generation interval 3.4709 3.3753 3.7233 3.7548 4.0004 3.6688 3.3544 Effective pop size 19.877 1146.1 105.68 53.455 n/a n/a n/a 6
Figure 3: a histogram ( tally distribution) of number of progeny per sire and dam over each of the seven 5-year blocks above. A longer tail on the distribution of progeny per sire is indicative of popular sires (few sires with a very large number of offspring, known to be a major contributor to a high rate of inbreeding). Figure 3: Distribution of progeny per sire (blue) and per dam (red) over 5-year blocks (1980-4 top, 2010-14 bottom). Vertical axis is a logarithmic scale. 7
Comments As with most breeds, the rate of inbreeding was at its highest in this breed in the 1980s and 1990s. This represents a genetic bottleneck, with genetic variation lost from the population. However, since the early-2000s the rate of inbreeding has been negative, implying moderate restoration of genetic diversity (possibly through the use of imported animals). It appears that the extensive use of popular dogs as sires has eased a little (the tail of the blue distribution shortening in figure 3). It should be noted that, while animals imported from overseas may appear completely unrelated, this is not always the case. Often the pedigree available to the Kennel Club is limited in the number of generations, hampering the ability to detect true, albeit distant, relationships. 8